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2. Try the latest version of tools.
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5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
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8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

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Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

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Exclude unescaped quote marks from GATK header?

I've recently run into an error running a pipeline on GATK SelectVariants-generated VCFs. The issue seems to be that SelectVariants (and perhaps other tools) leaves header line(s) containing multiple quotation marks internal to the line without escaping them (see example below). Is there already a way to exclude these problematic un-escaped quotation marks, or is this a fix that could be made so other programs can run more smoothly with GATK VCFs? Thanks!